Calculated Electron Affinities Research Articles

Structural basis for the temperature-induced transition of d-amino acid oxidase from pig kidney revealed by molecular dynamic simulation and photo-induced electron transfer

The structural basis for the temperature-induced transition in the D-amino acid oxidase (DAAO) monomer from pig kidney was studied by means of molecular dynamic simulations (MDS). The center to center (Rc) distances between the isoalloxazine ring (Iso) and all aromatic amino acids (Trp and Tyr) were calculated at 10 °C and 30 °C. Rc was shortest in Tyr224 (0.82 and 0.88 nm at 10 and 30 °C, respectively), and then in Tyr228. Hydrogen bonding (H-bond) formed between the Iso N1 and Gly315 N (peptide), between the Iso N3H and Leu51 O (peptide) and between the Iso N5 and Ala49 N (peptide) at 10 °C, whilst no H-bond was formed at the Iso N1 and Iso N3H at 30 °C. The H-bond of Iso O4 with Leu51 N (peptide) at 10 °C switched to that with Ala49 N (peptide) at 30 °C. The reported fluorescence lifetimes (228 and 182 ps at 10 and 30 °C, respectively) of DAAO were analyzed with Kakitani and Mataga (KM) ET theory. The calculated fluorescence lifetimes displayed an excellent agreement with the observed lifetimes. The ET rate was fastest from Tyr224 to the excited Iso (Iso*) at 10 °C and from Tyr314 at 30 °C, despite the fact that the Rc was shortest between Iso and Tyr224 at both temperatures. This was explained by the electrostatic energy in the protein. The differences in the observed fluorescence lifetimes at 10 and 30 °C were ascribed to the differences in electron affinity of the Iso* at both temperatures, in which the free energies of the electron affinity of Iso* at 10 and 30 °C were -8.69 eV and -8.51 eV respectively. The other physical quantities related to ET did not differ appreciably at both temperatures. The electron affinities at both temperatures were calculated with a semi-empirical molecular orbital method (MO) of PM6. Mean calculated electron affinities over 100 snapshots with 0.1 ps intervals were -7.69 eV at 10 °C and -7.59 eV at 30 °C. The difference in the calculated electron affinities, -0.11 eV, was close to the observed difference in the free energies, -0.18 eV. The present quantitative analysis predicts that the highest ET rate can occur from a donor with longer donor-acceptor distance, which was explained by differences in electrostatic energy.

Atomic properties of elements 114 and 118 and their adsorption on inert surfaces

We present fully relativistic coupled cluster calculations of ionization potentials, electron affinities, and polarizabilities of superheavy elements 114 and 118, along with their lighter homologues, lead and radon. The combination of the 4-component Dirac Hamiltonian with the state of the art coupled cluster approach allows us to achieve very good agreement with experimental values for the lighter elements; similar precision can be expected for our predictions for the superheavy atoms. The trends in the atomic properties are discussed, demonstrating the strong relativistic effects. Using the calculated atomic properties, adsorption enthalpies of the superheavy atoms on inert surfaces are estimated and shown to be rather low for both elements.

Calculated electron affinity and stability of halogen-terminated diamond

The chemical termination of diamond has a dramatic impact on its electrical and chemical properties, where hydrogen and oxygen termination produce negative and positive electron affinities, respectively. However, the impact of halogen termination is not fully understood. We show that for low-index surfaces, 100% fluorinated surfaces exhibit chemically stable positive electron affinities in the 1.17 to 2.63 eV range, whereas 100% chlorination is energetically unfavorable. At lower coverage the positive electron affinity is smaller, being a combination of halogen-terminated and unterminated sites. For mixed halogen and hydrogen termination, a wide range of negative and positive electron affinities can be achieved by varying the relative concentrations of adsorbed species. © 2011 American Physical Society.

Calculations of ionization energies and electron affinities for atoms and molecules: A comparative study with different methods

In the present work, we examined the performance of 36 density functionals, including the newly developed doubly hybrid density functional XYG3 (Y. Zhang, X. Xu, and W. A. Goddard III, Proc. Natl. Acad. Sci, USA, 2009, 106, 4963), to calculate ionization energies (IEs) and electron affinities (EAs). We used the well-established G2-1 set as reference, which contains 14 atoms and 24 molecules for IE, along with 7 atoms and 18 molecules for EA. XYG3 leads to mean absolute deviations (MADs) of 0.057 and 0.080 eV for IEs and EAs, respectively, using the basis set of 6-311 + G (3df,2p). In comparison with some other functionals, MADs for IEs are 0.109 (B2PLYP), 0.119 (M06-2X), 0.159 (X3LYP), 0.161 (PBE), 0.162 (B3LYP), 0.165 (PBE0), 0.173 (TPSS), 0.200 (BLYP), and 0.215 eV (LC-BLYP). MADs for EAs are 0.090 (X3LYP), 0.090 (B2PLYP), 0.102 (PBE), 0.103 (M06-2X), 0.104 (TPSS), 0.105 (BLYP), 0.106 (B3LYP), 0.126 (LC-BLYP), and 0.128 eV (PBE0).

Acetylenic Tetrathiafulvalene Scaffolds – Intramolecular Charge‐Transfer Molecules

AbstractTwo tetrathiafulvalene‐functionalized acetylenic scaffolds were synthesized by GlaserHay and Sonogashira coupling reactions; the one scaffold was based on a central dehydroannulene core and the other on a tetraethynylethene core. Peripheral propyl groups on the tetrathiafulvalenes ascertained solubility. The compounds are strong donoracceptor chromophores and exhibit characteristic charge‐transfer absorptions according to UV/VIS absorption spectroscopy. Furthermore, the redox properties were investigated by cyclic and differential‐pulse voltammetries. The experiments allow for a direct comparison between the acceptor strengths of the two acetylenic cores, and the conclusions are supported by electron‐affinity calculations.

Paradigms and paradoxes: what are the 54 electron affinities of O2?

Only one electron affinity of oxygen, 43(1) kJ mol−1 is generally cited since the molecular orbital theory anion bond order [3/4] gives an electron affinity, 14 kJ mol−1. However, electron correlation rules predict 27 bonding and 27 antibonding spin orbital coupling states. The relative bond orders (RBOs), 12/13 to [1/4] and the 13 valence electrons of superoxide are used to calculate electron affinities 103 to −243 kJ mol−1 consistent with experimental and theoretical values. These are used to construct 54 ionic Morse potentials.

Magnetic and electronic properties of the nickel clusters Ni n ( n ⩽ 30)

The magnetic property and electronic properties such as ionization potentials and electron affinities of the Ni n ( n ⩽ 30) neutral and ionic clusters have been studied using the density functional theory calculations with the PBE exchange–correlation energy functional. The variations of the calculated magnetic and ionization potential behaviors of the neutral Ni n ( n ⩽ 30) clusters are in good agreement with the experimental data. The tendency of the calculated electron affinity is generally consistent with but has small deviations from the experimental results.

Theoretical studies in the molecular Platonic solids: Pure and mixed carbon, nitrogen, phosphorus, and silicon tetrahedranes

AbstractCalculations were conducted at the G4MP2 and G4 composite method levels of theory on the 35 potential carbon, nitrogen, silicon, and phosphorus tetrahedrane derivatives with the general form C~a~N~b~Si~c~P~d~H~(4-b-d)~ (where a+b+c+d=4). At both levels of theory, optimized electronic ground state neutral singlet gas phase (298.15 K, 1 atm) geometries were obtained for 24 of the 35 possible C/N/Si/P tetrahedrane derivatives. Corresponding enthalpies of formation were calculated using the atomization method. Triplet state neutral tetrahedron starting geometries for all compounds either resulted in cage opening or failed to converge. Only 9 cationic and 3 anionic forms converged to stable geometries that retained the tetrahedron cage and were absent imaginary frequencies, thereby allowing the calculation of adiabatic ionization energies and electron affinities.

Novel quinonediimines derived from amino acid-like structures 1: Characterization and DFT computational study: N, N′-bis(5′-benzimidazolyl)-1,4-quinonediimine

Density functional calculations were performed on N, N′-bis(5′-benzimidazolyl)-1,4-quinonediimine, a novel substituted aniline “trimer”. This is the first reported symmetric quinonediimine with outer rings derived from amino-acid related structures. Results of the calculations were compared to experimental properties of the herein synthesized trimer. The calculated HOMO levels for isomers of the title compound range from −5.630 to −5.674 eV, and the LUMO levels from −2.889 to −2.924 eV. The calculated electron affinities range from 1.546 to 1.613 eV. The LUMO level is lowest and the electron affinity greatest in magnitude for the syn, syn (outer) isomer. Compared to the widely-studied aniline-capped aniline trimer N, N′-bis(4′-aminophenyl)-1,4-quinonediimine, the title compound has lower LUMO levels and greater electron affinity in both the emeraldine base or emeraldine dihydrochloride form, suggesting that it might be even more effective in corrosion control applications. Because the outer rings are derived from amino-acid related structures, such molecules, particularly as caps in polyanilines, could find use in biomedical applications.

Pharmacophore Modeling and Density Functional Theory Analysis for A Series of Nitroimidazole Compounds with Antitubercular Activity

In an attempt to highlight structural features required for potent antitubercular activity, five pharmacophoric features were developed for PA-824 and its analogs. The generated pharmacophore indicated importance of a nitro group, three hydrogen bond acceptor features, and a distal aromatic ring for potent activity. The model based on pharmacophore alignment has good correlation coefficient for the training set (r(2) = 0.81, SD = 0.31, F = 122.9, N = 152), which was evaluated using a test set (Q(2) = 0.77, root-mean-square error = 0.35, Pearson-R = 0.88, N = 49). Structure-activity relationship investigation further revealed that hydrophobic substitutions at the para-position of distal aromatic ring could lead to more potent analogs. The most active and inactive compounds were further studied using density functional theory at B3LYP/3-21*G level. The calculated electrostatic profile indicated that these compounds possess maximum negative potential in the vicinity of nitro group extending laterally to the imidazole ring. Furthermore, the calculated electron affinity values indicate the stability of radical anions, which could form upon one electron reduction in the biological system, thus, indicating the electron acceptor capacity of these compounds. Results of this study are expected to be useful in the design of novel potent nitroimidazoles as antitubercular agents.

Generation of Naphthoquinone Radical Anions by Electrospray Ionization: Solution, Gas-Phase, and Computational Chemistry Studies

Radical anions are present in several chemical processes, and understanding the reactivity of these species may be described by their thermodynamic properties. Over the last years, the formation of radical ions in the gas phase has been an important issue concerning electrospray ionization mass spectrometry studies. In this work, we report on the generation of radical anions of quinonoid compounds (Q) by electrospray ionization mass spectrometry. The balance between radical anion formation and the deprotonated molecule is also analyzed by influence of the experimental parameters (gas-phase acidity, electron affinity, and reduction potential) and solvent system employed. The gas-phase parameters for formation of radical species and deprotonated species were achieved on the basis of computational thermochemistry. The solution effects on the formation of radical anion (Q(•-)) and dianion (Q(2-)) were evaluated on the basis of cyclic voltammetry analysis and the reduction potentials compared with calculated electron affinities. The occurrence of unexpected ions [Q+15](-) was described as being a reaction between the solvent system and the radical anion, Q(•-). The gas-phase chemistry of the electrosprayed radical anions was obtained by collisional-induced dissociation and compared to the relative energy calculations. These results are important for understanding the formation and reactivity of radical anions and to establish their correlation with the reducing properties by electrospray ionization analyses.

Ab Initio Analysis and Harmonic Force Fields of Gallium Nitride Nanoclusters

Gallium nitride (GaN) clusters are analyzed to set approaches for more extended calculations at the nanoscale. We test the atom components and very small clusters using the most sophisticated compound methods such as G1−G3, CBS, W1, and a flavor of DFT (B3PW91) using several sizes and qualities of basis sets. Results are compared with very precise experimental information when available. Interestingly, the B3PW91 yields results comparable to the high-quality compound methods. For negative ions, it is difficult to assess the quality of the methods; the electron affinity (EA) calculations, as expected, yield better results when diffuse functions are used. All ionization potentials (IPs) are well reproduced by all methods, but the best results are obtained with B3PW91 for the Ga atom and with the compound methods for N. Among the compound methods, the W1 ones use the largest basis sets with 93 functions (which include two sets of g-functions) for one gallium atom. Geometry optimizations are performed with MP2 for the G-methods, HF for the CBS-methods (except QB3), and B3LYP for the CBS-QB3 and all W1 methods. G3 followed by B3PW91 yields the best result for the Ga quartet excited state, and there is little difference for the excited doublet of N, among the compound methods. In general all calculated IPs and EAs are in good agreement with existing experimental data. We also performed extended calculations of bigger GaN clusters such as GaxNy where 6 < x ≈ y < 19 using B3PW91/6-311G(d). Finally, we calculate second derivative and thus the vibrational spectra for all clusters studied. We generate harmonic force fields using the procedure Fuerza and averaged the force field parameters and use them in a simple heating molecular dynamics calculation that yields an acceptable value for the heat capacity.

Hybrid functional investigations of band gaps and band alignments for AlN, GaN, InN, and InGaN

Band gaps and band alignments for AlN, GaN, InN, and InGaN alloys are investigated using density functional theory with the with the Heyd-Scuseria-Ernzerhof {HSE06 [J. Heyd, G. E. Scuseria, and M. Ernzerhof, J. Chem. Phys. 134, 8207 (2003); 124, 219906 (2006)]} XC functional. The band gap of InGaN alloys as a function of In content is calculated and a strong bowing at low In content is found, described by bowing parameters 2.29 eV at 6.25% and 1.79 eV at 12.5%, indicating the band gap cannot be described by a single composition-independent bowing parameter. Valence-band maxima (VBM) and conduction-band minima (CBM) are aligned by combining bulk calculations with surface calculations for nonpolar surfaces. The influence of surface termination [(1100) m-plane or (1120) a-plane] is thoroughly investigated. We find that for the relaxed surfaces of the binary nitrides the difference in electron affinities between m- and a-plane is less than 0.1 eV. The absolute electron affinities are found to strongly depend on the choice of XC functional. However, we find that relative alignments are less sensitive to the choice of XC functional. In particular, we find that relative alignments may be calculated based on Perdew-Becke-Ernzerhof [J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 134, 3865 (1996)] surface calculations with the HSE06 lattice parameters. For InGaN we find that the VBM is a linear function of In content and that the majority of the band-gap bowing is located in the CBM. Based on the calculated electron affinities we predict that InGaN will be suited for water splitting up to 50% In content.

DFT/TDDFT Study on the electronic structures and optoelectronic properties of several red-emitting osmium(ii) complexes with different P∧P ancillary ligands

The ground and excited state geometries of several red-emitting phosphors (N^N)(2)Os(P^P) [where N^N = 5-(1-isoquinolyl)-1,2,4-triazoles, P^P = bis(dimethylphosphino)methylene(dmpm) (1); P^P = cis-1,2-bis-(dimethylphosphino)ethene(dmpe) (2); P^P = 1,2-bis(dimethylphosphino)benzene(dmpb) (3); P^P = 1,2-bis(dimethylphosphino)naphthalene(dmpn) (4); P^P = 1,2-bis(dimethylphosphino)-4-cyano-benzene(dmpcb) (5)] have been investigated by using the density functional theory (DFT) methods. The calculated results indicate that, for the studied complexes, the electron-transporting performance is better than the hole-transporting performance. The alteration of cis-P^P ancillary ligands with different conjugation lengths and substituents has an impact on the optoelectronic properties of these complexes, especially the electron-withdrawing group -CN in 5. The calculated energy gaps are nearly the same for complexes 1 to 4 (3.34 eV), while for 5, the HOMO and LUMO energies are lowered and the energy gap increases (3.42 eV). The absorption of 1 is red shifted, while that of 5 is blue shifted compared with the absorptions of 2, 3, and 4, which have similar absorptions. Complexes 2, 3, and 4 have almost identical emission wavelength 699 nm, while 1 (715 nm) and 5 (735 nm) are red shifted. The calculated electron affinities and reorganization energies indicate that complex 5 is the easiest for electron injection and has the best electron-transporting performance.

Joint photoelectron and theoretical study of (RhmCon)− (m = 1–5, n = 1–2) cluster anions and their neutral counterparts

Anion photoelectron spectroscopic experiments and calculations based on density functional theory have been used to investigate and uniquely identify the structural, electronic, and magnetic properties of both neutral and anionic (Rh(m)Co(n)) and (Rh(m)Co(n))(-) (m=1-5, n=1-2) clusters, respectively. Negative ion photoelectron spectra are presented for electron binding energies up to 3.493 eV. The calculated electron affinities and vertical detachment energies are in good agreement with the measured values. Computational results for geometric structures and magnetic moments of both cluster anions and their neutrals are presented.

Correlation of the first reduction potential of selected radiosensitizers determined by cyclic voltammetry with theoretical calculations

Radiosensitizers are drugs that make cancer cells more sensitive to radiation therapy. The cytotoxic properties of such compounds are due to the fact that in the cell these compounds undergo one-electron reduction to generate radical anions. Therefore, their theoretical and/or experimental study is of high interest. To determine the correlation between reduction potential determined by cyclic voltammetry measurements and some physicochemical properties of selected radiosensitizers theoretical calculations of electron affinities based on the DFT method with B3LYP functional at the level of 6-311++G** basis set in vacuum were utilized. Very good correlation was found between electron affinities of radiosensitizers and their reduction potential and so called E71 potential that account for the energy necessary to transfer the first electron to an electroactive group at pH 7 in aqueous medium to form a radical anion.

Theoretical study of new acceptor and donor molecules based on polycyclic aromatic hydrocarbons

Functionalized polycyclic aromatic hydrocarbons (PAHs) are an interesting class of molecules in which the electronic state of the graphene-like hydrocarbon part is tuned by the functional group. Searching for new types of donor and acceptor molecules, a set of new PAHs has recently been investigated experimentally using ultraviolet photoelectron spectroscopy (UPS). In this work, the electronic structure of the PAHs is studied theoretically with the help of B3LYP hybrid density functionals. Using the ΔSCF method, electron binding energies have been determined which affirm, specify and complement the UPS data. Symmetry properties of molecular orbitals are analyzed for a categorization and an estimate of the related signal strength. While σ-like orbitals are difficult to detect in UPS spectra of condensed film, calculation provides a detailed insight into the hidden parts of the electronic structure of donor and acceptor molecules. In addition, a diffuse basis set (6-311++G**) was used to calculate electron affinity and LUMO eigenvalues. The calculated electron affinity (EA) provides a classification of the donor/acceptor properties of the studied molecules. Coronene-hexaone shows a high EA, comparable to TCNQ, which is a well-known classical acceptor. Calculated HOMO–LUMO gaps using the related eigenvalues have a good agreement with the experimental lowest excitation energies. TD-DFT also accurately predicts the measured optical gap.

DFT/TD-DFT investigation of optical absorption spectra, electron affinities, and ionization potentials of mono-nitrated benzanthrones

Density functional theory (DFT) method B3LYP with basis sets 6-311+G(d,p), 6-31G(d) and 6-311G(d,p) have been used to compute molecular structures, UV–vis absorption spectra, electron affinities (EAs), and ionization potentials (IPs) of benzanthrone and 1-, 2-, 3-, 9-, 10-, and 11-nitrobenzanthrones. With the use of the time-dependent TD-B3LYP/6-311G(d,p) approach, the UV/vis absorption spectral bands, vertical excitation energies and oscillator strengths was studied. The calculated vertical excitation energies lie within <0.15 eV of the observed values. In comparison to benzanthrone, calculated absorption spectra of nitrated nitrobenzanthrones show red-shifting to >383 nm, which is correlated to their relative reactivity. Detailed clarification of the singlet-singlet excited states (and energies) are made. The calculated electron affinities are ∼0.5 eV greater than in benzanthrone (BA); being in the order 3-NBA > 10-NBA > 1-NBA > 2-NBA > 9-NBA > 11-NBA > BA. Similarly, ionization potentials follow a very close order in nitro-BAs. The calculated EAs and IPs implicate both reductive and oxidative pathways on transformation to mutagenic metabolites. The implications of the results are discussed in the context of their differential mutagenic potencies.

Synthesis, characterization, and computational study of N,N′-bis (2′,4′-dihydroxyphenyl)-1.4-quinonediimine, a hydroxyl-capped three-ring quinonediimine with sterically hindered substituent on outer rings

Density functional calculations were performed on N,N′-bis (2′,4′-dihydroxyphenyl)-1.4-quinonediimine, a hydroxyl-terminated quinonediimine with an additional meta-hydroxyl substituent on each outer ring. Results of the calculations were compared to experimental properties of the herein synthesized compound. The calculated LUMO levels for isomers of the title compound range from −2.764 to −3.279 eV. The calculated electron affinities range from 1.398 to 1.989 eV. Both the LUMO levels and electron affinities are greatest in magnitude for the syn, anti isomer. The HOMO levels, on the other hand, range from −5.383 eV (for the anti, anti isomer) to −5.541 eV (syn, anti). The predicted electronic transitions for the molecule in ethanol solvent correspond closely to those seen at 580 and 254 nm. The isomers vary widely in energy, leading to a marked preference for the syn, syn (outer) isomer – a direct result of the steric effect of the hydroxyl group at the 2′ position.

Influence of hydrogen bonding on hydrogen-atom abstraction reactions of dehydropyridinium cations in the gas phase.

The reactions of several substituted, positively charged dehydropyridinium cations with cyclohexane, methanol, and tetrahydrofuran have been examined in a Fourier-transform ion cyclotron resonance mass spectrometer. All of the charged monoradicals react with the neutral reagents exclusively via hydrogen atom abstraction. For cyclohexane, there is a good correlation between the reaction efficiencies and the calculated electron affinities at the radical sites; that is, the greater the electron affinity of the charged monoradical at the radical site, the faster the reaction. The reaction efficiencies with methanol and tetrahydrofuran, however, do not correlate with the calculated electron affinities. Density functional theory (DFT) calculations indicate that for these reagents a stabilizing hydrogen bonding interaction exists in the hydrogen atom abstraction transition states for some of the charged monoradicals but not for others. At both the MPW1K and G3MP2B3 levels of theory, there is a good correlation between the calculated activation enthalpies and the observed reaction efficiencies, although the G3MP2B3 method provides a slightly better correlation than the MPW1K method. The extent of enhancement in the reaction efficiencies caused by the hydrogen bonding interactions parallels the calculated hydrogen bond lengths in the transition states.